The present Małachowski School is the continuation of the Collegiate School opened at St. Michaels Collegiate Church in the year 1180. It was a church school until the year 1773. In this year it was taken over by the National Education Commission - the first ministry of education in the world, and since then it has been a state school. Its further fortunes and misfortunes are closely connected with the history of the country. The breaks in teaching were caused by the wars. After regaining Independence in 1918, the school was given the name of its present patron, Stanisław Małachowski - the co-author of Europe First Constitution.
After World War II the school introduced coeducational program for the first time on 18th February 1945.

Since then, 8100 students have graduated from the school. The most of the graduates have furthered their education in community colleges, polytechnical institutes and universities. 114 have become winners of the Polish National Olympiad, which are awards for students outstanding in their field. The best alumni are awarded the "Diligentiae" medals - after 18th century tradition. In the year 1979 the School was awarded the highest rank Polish order: the Commander Order Cross of Polonia Restituta with the Star.